I've run into this many many times in my 50 years of fixin stuff. Usually the toughest ones have the stupidest or simplest problem when you finally find it. The toughest battery charging problem I ever had was the first, in 1973. We tried everything and one day the boss walked in and said "hook the battery up backwards". Turned out the customer had charged it backwards but connected it red to red, black to ground. I wasn't much of an electrical guy then and didn't even own a VOM let alone know how to use it. I've since learned on the tough ones to start on one end with a VOM, use the troubleshooter flow chart if there is one, and go step by step from the battery out to, or from the problem back to it, documenting the results. Troubleshoot in one direction only, don't jump around except for a very few preliminary tests. On something that won't start it's harder and but have someone hit the starter button and watch for spark while you move harnesses around, flexing them as they do in operation, in the steering area, controls, near suspensions, or anywhere there can be movement. You might be beyond any more efforts, but maybe the next time you run into a tough one this will help.